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- PDB-4l9z: Crystal Structure of Rhodobacter sphaeroides malyl-CoA lyase in c... -

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Basic information

Entry
Database: PDB / ID: 4l9z
TitleCrystal Structure of Rhodobacter sphaeroides malyl-CoA lyase in complex with magnesium, oxalate, and CoA
ComponentsMalyl-CoA lyase
KeywordsLYASE / TIM barrel
Function / homology
Function and homology information


malyl-CoA lyase / L-erythro-3-methylmalyl-CoA lyase activity / malyl-CoA lyase activity / (S)-citramalyl-CoA lyase / (S)-citramalyl-CoA lyase activity / metal ion binding
Similarity search - Function
Citrate lyase beta subunit-like / HpcH/HpaI aldolase/citrate lyase domain / HpcH/HpaI aldolase/citrate lyase family / Phosphoenolpyruvate-binding domains / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
COENZYME A / OXALATE ION / L-malyl-CoA/beta-methylmalyl-CoA lyase
Similarity search - Component
Biological speciesRhodobacter sphaeroides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.011 Å
AuthorsZarzycki, J. / Kerfeld, C.A.
CitationJournal: Bmc Struct.Biol. / Year: 2013
Title: The crystal structures of the tri-functional Chloroflexus aurantiacus and bi-functional Rhodobacter sphaeroides malyl-CoA lyases and comparison with CitE-like superfamily enzymes and malate synthases.
Authors: Zarzycki, J. / Kerfeld, C.A.
History
DepositionJun 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Malyl-CoA lyase
B: Malyl-CoA lyase
C: Malyl-CoA lyase
D: Malyl-CoA lyase
E: Malyl-CoA lyase
F: Malyl-CoA lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)226,43724
Polymers221,1586
Non-polymers5,27918
Water45,5062526
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area42220 Å2
ΔGint-223 kcal/mol
Surface area56960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)221.509, 221.509, 96.262
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein
Malyl-CoA lyase / / (3S)-malyl-CoA/beta-methylmalyl-CoA lyase / L-malyl-CoA/beta-methylmalyl-CoA lyase


Mass: 36859.684 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Strain: ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158 / Gene: mcl1, RHOS4_03500, RSP_1771 / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q3J5L6, malyl-CoA lyase
#2: Chemical
ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical
ChemComp-OXL / OXALATE ION / Oxalate


Mass: 88.019 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2O4
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2526 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.31 Å3/Da / Density % sol: 62.84 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1 part protein solution (7.5 mg/mL in 20 mM Tris-HCl, pH 7.5, 2 mM magnesium chloride, 100 mM sodium chloride) + 2 parts buffer (0.1 M HEPES/NaOH, pH 7.5, 0.1 M magnesium chloride, 10% w/v ...Details: 1 part protein solution (7.5 mg/mL in 20 mM Tris-HCl, pH 7.5, 2 mM magnesium chloride, 100 mM sodium chloride) + 2 parts buffer (0.1 M HEPES/NaOH, pH 7.5, 0.1 M magnesium chloride, 10% w/v PEG4000) + 1 part substrate solution (20 mM Tris-HCl, pH 7.5, 2 mM magnesium chloride, 100 mM sodium chloride, 20 mM propionyl-CoA, 25 mM sodium oxalate), VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.977408 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 30, 2012
RadiationMonochromator: Asymmetric curved crystal Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977408 Å / Relative weight: 1
ReflectionResolution: 2.011→38.455 Å / Num. all: 175339 / Num. obs: 175339 / % possible obs: 98.3 % / Redundancy: 6.4 % / Rsym value: 0.158 / Net I/σ(I): 11.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.011-2.126.30.7441160281256410.74499
2.12-2.256.30.521.5154139243560.5299.2
2.25-2.46.40.3892145369228780.38998.9
2.4-2.66.40.2922.7135550212730.29298.8
2.6-2.846.40.2113.7124819195230.21198.4
2.84-3.186.40.1375.6112215175370.13797.9
3.18-3.676.40.0888.898543154320.08897.2
3.67-4.56.30.05812.982103130050.05896.9
4.5-6.366.60.0491566789101190.04996.8
6.36-38.4556.50.03419.83647055750.03495.6

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHENIX1.8.2_1303refinement
PDB_EXTRACT3.11data extraction
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4L9Y

4l9y


Resolution: 2.011→38.455 Å / Occupancy max: 1 / Occupancy min: 0.44 / SU ML: 0.2 / σ(F): 0.86 / Phase error: 19.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.194 1744 1.15 %
Rwork0.1699 --
obs0.1702 175323 91.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 80.95 Å2 / Biso mean: 16.0823 Å2 / Biso min: 2.09 Å2
Refinement stepCycle: LAST / Resolution: 2.011→38.455 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14274 0 330 2526 17130
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00614934
X-RAY DIFFRACTIONf_angle_d0.88120316
X-RAY DIFFRACTIONf_chiral_restr0.0592223
X-RAY DIFFRACTIONf_plane_restr0.0032661
X-RAY DIFFRACTIONf_dihedral_angle_d12.8995514
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.011-2.0370.33411410.2621117231186488
2.037-2.06490.25591360.2488121431227991
2.0649-2.09440.2541560.241121321228891
2.0944-2.12570.25711490.2321122081235791
2.1257-2.15890.2751440.2266121891233391
2.1589-2.19430.24741390.2238122161235591
2.1943-2.23210.23331340.2079121341226891
2.2321-2.27270.2151390.2085122121235192
2.2727-2.31640.21331450.2003122491239491
2.3164-2.36370.25021480.1932122991244792
2.3637-2.41510.22281290.1973122381236792
2.4151-2.47120.24141390.1843122391237892
2.4712-2.5330.20631430.1858122931243692
2.533-2.60150.19241520.1798123271247992
2.6015-2.6780.21431430.1759122471239092
2.678-2.76440.20471390.1718123121245192
2.7644-2.86320.23351410.1709123431248492
2.8632-2.97780.15441370.1637123301246792
2.9778-3.11330.18411560.1562123291248592
3.1133-3.27730.15061380.1491123401247893
3.2773-3.48260.14521380.149123451248392
3.4826-3.75120.15671410.1344123981253993
3.7512-4.12830.15171460.1288123511249792
4.1283-4.72480.15021380.1242124011253993
4.7248-5.94920.16451430.1404124761261994
5.9492-38.46190.18321430.1561125331267694

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